.. _example mper-tm viral bilayer:

Example 17: HIV-1 Env MPER-TM Trimer in an Asymmetric, Model Viral Bilayer
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.. figure:: my_6e8w_viral.png

           HIV-1 gp41 (MPER-TM) trimer embedded in a model viral envelope lipid bilayer.  Bilayer is clipped to show the protein, and each protein chain is colored uniquely.  The outer leaflet (top) is composed of 36% Sphingomyelin d18:1/16:0 (CHARMM residue name PSM, colored grey), 17% 3-palmitoyl-2-oleoyl-D-glycero-1-Phosphatidylcholine (POPC, green), and 43% cholesterol (CHL1, white).  The inner leaflet (bottom) is composed of 30% 1-Stearoyl-2-Oleoyl-Phosphatidylethanolamine (SOPE, purple), 18% 1-Stearoyl-2-Oleoyl-Phosphatidylserine (SOPS, blue), 9% 3-palmitoyl-2-oleoyl-D-glycero-1-Phosphatidylethanolamine  (POPE, pink), and 47% cholesterol.


This example is the same as :ref:`example mper-tm symmetric bilayer`, but uses a model viral bilayer instead of a DMPC bilayer.  The model viral bilayer is constructed from a mixture of lipids that are commonly found in the viral membrane.

.. literalinclude:: ../../../../pestifer/resources/examples/ex17/inputs/hiv-mpertm3-membrane2.yaml

.. task-table:: ../../../../pestifer/resources/examples/ex17/inputs/hiv-mpertm3-membrane2.yaml


Results
+++++++

The plots below are generated by default during the membrane-building process.

.. figure:: 17-patchA-a_x-b_y-c_z.png

           Cell dimensions vs time step for the initial symmetric 200-lipid bilayer patch from which the upper leaflet is extracted.

.. figure:: 17-patchB-a_x-b_y-c_z.png

           Cell dimensions vs time step for the initial asymmetric 200-lipid bilayer patch from which the lower leaflet is extracted.

.. figure:: 17-patchA-density.png

           System density vs time step for the initial 200-lipid bilayer patch from which the upper leaflet is extracted.

.. figure:: 17-patchB-density.png

            System density vs time step for the initial 200-lipid bilayer patch from which the lower leaflet is extracted.

.. figure:: 17-patchA-pressureprofile.png

           Pressure profiles for selected time intervals during relaxation of the upper leaflet bilayer patch.

.. figure:: 17-patchB-pressureprofile.png

              Pressure profiles for selected time intervals during relaxation of the lower leaflet bilayer patch.

The ``mdplot`` task generated the following plots for the membrane-embedded system.

.. figure:: 17-bilayer-a_x-b_y-c_z.png

           Cell dimensions vs time step for the protein-embedded membrane.

.. figure:: 17-bilayer-density.png

           System density vs time step for the protein-embedded membrane.

.. figure:: 17-bilayer-pressureprofile.png

           Pressure profiles for selected time intervals during the protein-embedded membrane relaxation.
.. raw:: html

    <div class="autogen-footer">
        <p>Example author: Cameron F. Abrams &nbsp;&nbsp;&nbsp; Contact: <a href="mailto:cfa22@drexel.edu">cfa22@drexel.edu</a></p>
    </div>